The Genome of the Cauliflower Coral Pocillopora verrucosa

Abstract

Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) is comprised of repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.

De novo Assembly of the Brain Coral Platygyra sinensis Genome

“…We discovered that 50.03% of the genome assembly was occupied by repetitive elements, most of which were unclassified repeats (29.28%) and DNA elements (10.79%). The proportion of repetitive sequences in the brain coral was higher than the figures reported for A. millepora (34.55%) (Ying et al, 2019) and P. verrucosa (41.22%) (Buitrago-López et al, 2020) but comparable to the number reported for Pachyseris speciosa (52.5%) (Bongaerts et al, 2021).…”

“…Little is known about the responses of the brain coral genus Platygyra to heat stress at the molecular level due to the lack of genomic/transcriptomic resources. The availability of genomic and transcriptomic data from a number of coral species allows us to probe the molecular stress response of the organisms to biotic and abiotic stress conditions (Shinzato et al, 2011;Traylor-Knowles et al, 2011;Kenkel et al, 2013;Kitchen et al, 2015;Davies et al, 2016;Buitrago-López et al, 2020). Here, we report the first reference genome assembly for the brain coral P. sinensis using long-read Pacific Biosciences sequencing technology.…”

Cophylogeny and specificity between cryptic coral species (Pocilloporaspp.) at Mo’orea and their symbionts (Symbiodiniaceae)

“…The number of raw reads obtained per library ranged from 326,778 – 7,780,151. After trimming, the number of reads that mapped to the P. verrucosa genome (Buitrago-López et al 2020) using ipyrad v0.9.60 (Eaton and Overcast 2020) ranged from 101,804 – 6,146,286 per library, with the number of loci in the concatenated genomic dataset ranging from 176 – 17,689 among samples, resulting in a sequence matrix consisting of 92.5% missing sites. ExaBayes v1.4.1 (Aberer et al 2014) with default parameters was used to generate a Bayesian phylogeny of this concatenated genomic loci dataset.…”

A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity

“…To date, our understanding of the molecular biology of stony corals largely derives from genome sequencing efforts. These data have provided crucial information on coral population structure ( Dixon et al, 2015 ; Fuller et al, 2020 ; Shinzato et al, 2021 ) and on the evolution of coral gene repertoires, including genes potentially involved in symbiosis, skeleton-formation, and immunity ( Barshis et al, 2013 ; Bayer et al, 2012 ; Bhattacharya et al, 2016 ; Buitrago-López et al, 2020 ; Shinzato et al, 2011 ; Voolstra et al, 2017 ; Ying et al, 2018 ). However, fundamental aspects of stony coral biology are still to be clarified: the specific cellular context in which these genes are employed and the diversity of cell types encoded in scleractinian genomes.…”